User:Rfriedman - Revision history

Rfriedman: /* 2009 */

2009-05-08T17:51:56Z

‎2009

Show changes

Smith: /* 2006 */

2009-05-07T21:35:07Z

‎2006

Smith: /* 2009 */

2009-05-07T21:27:07Z

‎2009

Smith: /* 2009 */

2009-05-07T21:24:36Z

‎2009

Smith: /* 2007 */

2009-05-07T21:01:04Z

‎2007

Smith: /* 2006 */

2009-05-07T20:33:56Z

‎2006

Smith: /* 2006 */

2009-05-07T20:28:23Z

‎2006

Rfriedman: /* Tutorials Comments */

2009-05-07T20:05:11Z

‎Tutorials Comments

Rfriedman: /* 2009 */

2009-05-07T20:01:13Z

‎2009

Rfriedman: /* Tutorials Comments */

2009-05-07T19:58:13Z

‎Tutorials Comments

@@ Line 107: / Line 107: @@
 would be helpful.
-/11/06 A good filter feature would be to give the user an option of accepting or
+/11/06 ('''answer - entered as addition to feature request 1845).  A good filter feature would be to give the user an option of accepting or
 rejecting the filtering based upon the number that survived the filtering prior
 to acceptance. Also, there should be the option of blowing up the heatmap. In

@@ Line 451: / Line 451: @@
 the change as a whole could be sorted by statistical signficance.
-/05/09 1.63 (answer -  The dataset history for the node will show what was actually done.  The node name indicates where the data came from, in this case the t-test component. Maybe we could make it say "t-test - permutations". Noted as feature request 1857).   Differential expression. The results node is reported as a t-test,
+/05/09 1.63 ('''answer -  The dataset history for the node will show what was actually done.  The node name indicates where the data came from, in this case the t-test component. Maybe we could make it say "t-test - permutations". Noted as feature request 1857''').   Differential expression. The results node is reported as a t-test,
 even if it is a permutation test. I suggest to change label permutation tests,
 Random permutations, or All permutations, depending on which option is chosen.

@@ Line 428: / Line 428: @@
-/5/09 1.63. Ken suggested that I try array-train.nci.nih.gov,
+/5/09 1.63. ['''answer - could not reproduce Richard's problem, may be something about the Mac.  Will add to tests for 1.7 release''') Ken suggested that I try array-train.nci.nih.gov,
 as a test case for remote databases, but it now requires a password.
 I suggest that the “Remote database” button be removed from the general
@@ Line 437: / Line 437: @@
 if you are interested).
-/05/09 1.63 Color Mosiac: The ability to switch between absolute
+/05/09 1.63 ('''answer - feature request 1855''') Color Mosaic: The ability to switch between absolute
 and relative expression mode without rebooting would be useful.
-/05/09 1.63 The ability to label array names (not just array groups).
+/05/09 1.63 ('''answer - feature request 1856''') The ability to label array names (not just array groups).
 In the color mosiac would also be useful.
-/05/09 1.63 Microarray viewer - gene profile. The image snapshot and
+/05/09 1.63 ('''answer - image snapshot (right-click menu) does work for me in the development version.  lightbulb is not present''').  Microarray viewer - gene profile. The image snapshot and
 the lightbulb (view graph details with mouse move-over) don't work.
@@ Line 451: / Line 451: @@
 the change as a whole could be sorted by statistical signficance.
-/05/09 1.63 Differential expression. The results node is reported as a t-test,
+/05/09 1.63 (answer -  The dataset history for the node will show what was actually done.  The node name indicates where the data came from, in this case the t-test component. Maybe we could make it say "t-test - permutations". Noted as feature request 1857).   Differential expression. The results node is reported as a t-test,
 even if it is a permutation test. I suggest to change label permutation tests,
 Random permutations, or All permutations, depending on which option is chosen.
@@ Line 458: / Line 458: @@
 (class comparison) clustering (class discovery) and classifiers (class prediction).
-/06/09 1.63 Bioconductor outputgene expression files cannot be read in using the
+/06/09 1.63 ('''answer - can you alter the bioconductor output settings to create a file we can use?''') Bioconductor output gene expression files cannot be read in using the
 RMAexpress output format. I get the following error message.
 [[Image:Rmaerror.png]]

@@ Line 261: / Line 261: @@
 or patterns highlighted in sequences.
-/13/07 1.06 (answer - now using caGrid services, only available are shown)I think that the Globus check box should be removed until such time that Globus
+/13/07 1.06 ('''answer - fixed: now using caGrid services, only available are shown''')I think that the Globus check box should be removed until such time that Globus
 is available.
@@ Line 357: / Line 357: @@
 an only be restored when they are functional.
-/19/07 1.06 Promoter. This is a good tool but it might not be state of the art.
+/19/07 1.06 ('''answer: entered as feature request 1852''')  Promoter. This is a good tool but it might not be state of the art.
 The emphasis in promoter searching has shifted to using methods of finding conserved
 and reducing the noise by limiting the search to conserved regions.
@@ Line 368: / Line 368: @@
 Another point is that these tools search a databases of sites, not a few selected sites.
-Another point is that it would be bettwer if the program to take gene names  as input and found the promoters as other programs do.
+Another point is that it would be better if the program to take gene names  as input and found the promoters as other programs do.
@@ Line 387: / Line 387: @@
 the menu.
-/26/07 1.06. the user currently has a choice of either equal
+/26/07 1.06. ('''answer: entered as feature request 1853''' ) The user currently has a choice of either equal
 variance or unequal variance t-tests. This can be
 distinguished by the test for equality of variances (Bartlett test).
-/16/07 1.06log2 transform I got an error message: This data
+/16/07 1.06 ('''answer - this is the way the webmatrix data came to us from the lab.  You can fix the data using the threshold normalizer or quantile normalization''').  log2 transform I got an error message: This data
 contains non-positve data points. This should not be with
 raw mas5 data.
-/26/07 1.06 In the heat map generated by hierarchical clustering markers (probesets) are labelled by their Affymetrix probeset id which is not very informative. We need a way to display the names of the genes. Otherwise, this is much less useful  that cluster 3.0 and JavaTreeview which can be confgured to display both gene names and probesets and be linked to web accessible databases.
+/26/07 1.06 ('''answer - this has already been fixed''')   In the heat map generated by hierarchical clustering markers (probesets) are labelled by their Affymetrix probeset id which is not very informative. We need a way to display the names of the genes. Otherwise, this is much less useful  that cluster 3.0 and JavaTreeview which can be confgured to display both gene names and probesets and be linked to web accessible databases.
 /26/07 ('''answer - this is available as option "both"''') 1.06 The ability to simultaneously cluster probesets and
 phenotypes would also be useful.
-/28/07 1.06 The marker annotation feature doesn't really
+/28/07 1.06 ('''answer - A: we could add the gene symbol.  The spelled-out gene name is already displayed.  A, B and C: entered as feature request  1854''' ) The marker annotation feature doesn't really
 improve the usability much for a number of reasons.
@@ Line 416: / Line 416: @@
 I am wondering if Entrez gene could be added as well.
-C. The cGAP pathways, whereas they supplement KEGG pathways are not as good. Some of them in fact are too small to be useful.  I suggest that KEGG pathways be added as well.
+C. The cGAP pathways, whereas they supplement KEGG pathways, are not as good. Some of them in fact are too small to be useful.  I suggest that KEGG pathways be added as well.
 ==2009==

@@ Line 113: / Line 113: @@
 and JavaTreeview should be reproduce for clustering.
-/14/06 (answer - feature request 1850) A word about t-tests. It is very common in the microarray field for
+/14/06 ('''answer - entered as feature request 1850''') A word about t-tests. It is very common in the microarray field for
 experimentalists to not give sufficient numbers of replicates to get good statistics. The word in the statistical community is to use some variant of
 a Bayesian t-test which pools variances of similar sample sizes to take into
@@ Line 135: / Line 135: @@
 therefore can be ported to geWorkbench as part of a of a general Bioconductor port.
-/14/06 i strongly recommed that the benjamini-Hochberg False discovery rate
+/14/06 ('''answer - a long-standing wish - entered as feature request 1851''')  i strongly recommed that the benjamini-Hochberg False discovery rate
 correction be offered as an option. In fact all of the options in the current
 version of AffyLmGUI would find use.
@@ Line 142: / Line 142: @@
 display on the t-test output.
-/15/06 With respect to the multiple t-test, an obvious improvement, alluded to
+/15/06 ('''answer - component discontinued''') With respect to the multiple t-test, an obvious improvement, alluded to
 in the functionality write-up is to take into account multiple comparisons. The
 most basic way to do this is to add terms corresponding to the variance of
@@ Line 174: / Line 174: @@
 The Workbench should remind the user frequently of unspecified and unnotated files.
-/28/06 A much larger assortment of chip-types should be offered.
+/28/06 ('''answer - we know''') A much larger assortment of chip-types should be offered.
 ?28/06- A general functionality need is the ability to analyze SNP-chips

@@ Line 20: / Line 20: @@
 /7/06 ('''answer: feature request 1844''') I suggest asking "are you sure" when a user asks to remove a project.
-/26/06 It  would be very helpful if the workbench could display an hourglass, or a watch, or a sundial or something, when it ia loading or working - for example when it
+/26/06 (answer - already implemented for remote file download and all analyses) It  would be very helpful if the workbench could display an hourglass, or a watch, or a sundial or something, when it ia loading or working - for example when it
 is loading micorarray files from a remote database.
@@ Line 29: / Line 29: @@
 /25/06 The two tutorial sets should be included in the download automatially.
-/25/06 I would like to ammend my recommendation of 4/26/06 to inlcude an estimate of
+/25/06 ('''answer - that would be nice - if we had some way of knowing...no action for now.''') I would like to ammend my recommendation of 4/26/06 to inlcude an estimate of
 the time a task will take, so that people may use it more easily.
-/25/06 When I spoke to the group, Ken had stated that the intensities in the
+/25/06 ('''answer - if you can think of a better name, we can consider it!''') When I spoke to the group, Ken had stated that the intensities in the microarray viewer did not correspond to an image of the chip. In which  case the phrase "microarray viewer" is misleading. In fact I am not sure to what the intensities an spacing in microarray viewer corresponds.
 /25/06 ('''answer - already changed to "show arrays"''')I think that "Get bioassays" is a poor command on 2 grounds:
@@ Line 48: / Line 45: @@
 are being loaded.
-/25/06 I suggest that a dummy new source be made available to the users to learn how
+/25/06 ('''answer - caArray now provides access to a staging instance as well as a training instance.  geWorkbench does not upload data to remote sources''')  I suggest that a dummy new source be made available to the users to learn how
-to access a remote source and I suggest that intructions for posting a remote source
+to access a remote source and I suggest that instructions for posting a remote source
 be made available. Doing these things will increase the ease with which users
 can use the workbench in collaborative projects.
@@ Line 61: / Line 58: @@
 defintions in a controlled vocabulary.
-/31/06 ('''answer - now uses array name.  the items mentioned can be searched in the Markers component.''') With respectto the tabular microarray view. There is also a
+/31/06 ('''answer - now uses array name.  The items mentioned can be searched in the Markers component.''') With respect to the tabular microarray view. There is also a
-"probe number" for affy chips (1,2,3. ..) based upon its poistion in a sort.
+"probe number" for affy chips (1,2,3. ..) based upon its position in a sort.
 It would be useful to have a colum for that. It would also be useful to have
 seperate, searchable columns for the following 3 items:
@@ Line 84: / Line 81: @@
 or "flter-out values inside range".
-/29/06 	I recently did some Hierarchical Clustering using Cluster 3.0.
+/29/06 ('''answer - can't follow what is meant''') I recently did some Hierarchical Clustering using Cluster 3.0.
-Instead of simply filtering by absolulte M value, its also enables the
+Instead of simply filtering by absolute M value, its also enables the
-user to retain genes that are larger than a given mvalue in a user-specifiiable
+user to retain genes that are larger than a given m value in a user-specifiable
 # of experiments. It also offers the following options:
-. %. present >= of chips (this only works if you use present/absent threshholds rather than
+. % present >= of chips (this only works if you use present/absent thresholds rather than
 statistical noise.
-.SD gene vector >=X to remove genes with insufficient variability.
+. SD gene vector >=X to remove genes with insufficient variability.
 . Max-Min >= another variability filter.
 I can see why someone might want to use 2 or 3.
-/17/06 Tabular micorarray format - The column widths on the tabular microarray format
+/17/06 Tabular microrarray format - The column widths on the tabular microarray format
-should be suffcient to accomodate the whole title of the chip.
+should be sufficient to accommodate the whole title of the chip.
-/17/06 The color mosiac only makes sense if the data already has a log2 or other
+/17/06 ('''answer - this is really up to the user.  We can mention this in the tutorial''') The color mosaic only makes sense if the data already has a log2 or other
 variance-stabilization transformation. As is, an unsuspecting user can look at real values
-at this can be confusing. Furthermore, heatmaps make teh most sense for log ratio
+at this can be confusing. Furthermore, heatmaps make the most sense for log ratio
-comarisons versus a standard.
+comparisons versus a standard.
-/8/06 The tabular micorarray viewer should be saveable as an Excel spreadsheet.
+/8/06 ('''answer - it is just a viewer of data one already has.  We could perhaps add new "Save as" options to the Project folders component for microarry data, for example, tab-delimited rather than just "exp" format.  But in this case, the array sets would be lost.... feature requeset 1849''')   The tabular micorarray viewer should be savable as an Excel spreadsheet.
-all tables should be saveable as an excel spreadsheets.
+all tables should be savable as an excel spreadsheets.
 /10/06 A linear or spline fit to the reference line in the scatterplot
@@ Line 116: / Line 113: @@
 and JavaTreeview should be reproduce for clustering.
-/14/06 A word about t-tests. It is very common in the microarray field for
+/14/06 (answer - feature request 1850) A word about t-tests. It is very common in the microarray field for
 experimentalists to not give sufficient numbers of replicates to get good statistics. The word in the statistical community is to use some variant of
 a Bayesian t-test which pools variances of similar sample sizes to take into
@@ Line 142: / Line 139: @@
 version of AffyLmGUI would find use.
-/14/06 I suggest that the heat map ratehr than the volcnaoc plot be the default
+/14/06 I suggest that the heat map rather than the volcano plot be the default
-display onb the t-test output.
+display on the t-test output.
 /15/06 With respect to the multiple t-test, an obvious improvement, alluded to

@@ Line 806: / Line 806: @@
 and a modulator file available in tutorial data be specified.
-/0/09 1.63 MINDy 02/04/09
+/07/09 1.63 MINDy 02/04/09
 I suggest that the tutorial exercise include the saving of the target genes.

@@ Line 474: / Line 474: @@
 as targets, and I try to get a heat map, I get an error message:
-There is not enough memory to dispaly the heatmap.
+There is not enough memory to display the heatmap.
 ==Tutorials Comments==

@@ Line 797: / Line 797: @@
 into the ARACNE tutorial.
-/00/09 1.63 MINDy 02/04/09
+/07/09 1.63 MINDy 02/04/09
 I suggest that the tutorial exercise be made more explicit, with a hub gene
 and a modulator file available in tutorial data be specified.